Variant rs716501 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.29 in 151,946 control chromosomes in the GnomAD database, including 7,536 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 7536 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.970

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44048

AN:

151828

Hom.:

7535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.478

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.290

AC:

44050

AN:

151946

Hom.:

7536

Cov.:

AF XY:

0.297

AC XY:

22045

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.396

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.478

Gnomad4 SAS

AF:

0.263

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.338

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.322

Hom.:

4584

Bravo

AF:

0.280

Asia WGS

AF:

0.298

AC:

1031

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.79

DANN

Benign

0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over